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MolSysMT 0.11.3 documentation - Home MolSysMT 0.11.3 documentation - Home
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  • About
  • Showcase
  • User guide
  • Developer guide
  • API documentation
  • AI Assistants
  • GitHub

Section Navigation

  • Introduction
    • What’s MolSysMT?
    • Installation
    • Molecular systems
      • Description
      • Items and forms
      • Forms
      • Elements
      • Attributes
    • Demo Systems
    • Native forms
      • file:h5msm
    • Selection syntaxes
    • Tools
    • Viewers
    • Supported
    • Memory management
    • Quantities and units
    • Configuration options
    • MolSysMT Logging Setup — User Guide
  • Tools
    • Basic
      • Add
      • Append structures
      • Are multiple molecular systems
      • Compare
      • Concatenate structures
      • Contains
      • Convert
      • Copy
      • Extract
      • Get attributes
      • Get form
      • Get label
      • Get
      • Has attribute
      • Info
      • Is a molecular system
      • Is composed of
      • Iterator
      • Merge
      • Remove
      • Select
      • Set
      • View
      • Where is attribute
    • Build
      • Add bonds
      • Add missing bonds
      • Add missing heavy atoms
      • Add missing hydrogens
      • Add missing terminal cappings
      • Build peptide
      • Define new chain
      • Get disulfide bonds
      • Get missing bonds
      • Get missing heavy atoms
      • Get missing residues
      • Get missing terminals
      • Get non standard residues
      • Has hydrogens
      • Is solvated
      • Make bioassembly
      • Make water box
      • Mutate
      • Remove overlapping molecules
      • Solvate
      • Solve atoms with alternate locations
    • Topology
      • Get bondgraph
      • Get covalent blocks
      • Get covalent chains
      • Get dihedral quartets
      • Get sequence alignment
      • Get sequence identity
    • Structure
      • Center
      • Flip
      • Get angles
      • Get center
      • Get contacts
      • Get dihedral angles
      • Get distances
      • Get least RMSD
      • Get maximum distances
      • Get minimum distances
      • Get neighbors
      • Get geometric axis
      • Get radius of gyration
      • Get RMSD
      • Least RMSD align
      • Least RMSD fit
      • Move away
      • Principal component analysis
      • Rotate
      • Set dihedral angles
      • Shift dihedral angles
      • Show contacts
      • Translate
    • Periodic boundary conditions
      • Get angles from vectors
      • Get boxfrom lengths and angles
      • Get lengths and angles from box
      • Get lengths from box
      • Get shape from box
      • Shape from angles
      • Angles from vectors
      • Get volume from box
      • Has PBC
      • Unwrap
      • Wrap to MIC
      • Wrap to PBC
    • Physical and chemical properties
      • Get area buried
      • Get atomic radius
      • Get buried fraction
      • Get charge
      • Get hydrophobicity
      • Get mass
      • Get polarity
      • Get SASA
      • Get surface area
      • Get transmembrane tendency
      • Get volume
    • Hydrogen bonds
      • Get acceptor atoms
      • Get donor atoms
    • Molecular mechanics
      • Get forces
      • Potential energy minimization
      • Get non bonded potential energy
      • Get potential energy
    • Element
      • Atom
        • Get atom type from atom name
      • Molecule
        • Get bonded atom pairs
        • Get group type
        • Is group type
      • Component
        • Get component id
        • Get component index
        • Get component name
        • Get component type
        • Get number of components
        • Is component type
      • Molecule
        • Get molecule id
        • Get molecule index
        • Get molecule name
        • Get molecule type
        • Get number of molecules
        • Is component type
      • Entity
        • Get entity id
        • Get entity index
        • Get entity name
        • Get entity type
        • Get number of components
      • Chain
        • Get chain type
    • Form
      • Get attributes
      • Has attribute
    • Thirds
      • NGLView
        • Add arrows
        • Add contacts
        • Add cylinders
        • Add hbonds
        • Set color by value
        • Show as balls and sticks
        • Show as licorice
        • Show as surface
      • OpenMM
        • Custom External Forces
        • Reporters
  • Cookbook
    • Barnase-Barstar
    • Working with OpenMM
    • Working with NGLView
  • User guide
  • Tools
  • Molecular mechanics

Molecular mechanics#

  • Get forces
  • Potential energy minimization
  • Get non bonded potential energy
  • Get potential energy

previous

Get donor atoms

next

Get forces
© 2025, Liliana M. Moreno Vargas, Diego Prada Gracia and contributors | UIBCDF Lab at the Children's Hospital of Mexico Federico Gómez
MolSysMT is an open source project shared under an MIT license with a structure based on the Computational Molecular Science Python Cookiecutter version 1.5

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